DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet. 2008;9:465-476. [PMID: 18463664 DOI: 10.1038/nrg2341]

Biomarkers in lung cancer treatment

Lung carcinoma (LC) is the primary cause of millions of deaths worldwide. As LC is typically diagnosed at a later stage, its prevention and treatment are difficult. The pathological basis of both types of LC, namely non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC), is highly determined. The only treatments available for LC are surgical resection and chemotherapy, which require sophisticated new treatments. Biomarkers are promising treatment options, because they can be used for both diagnosis and treatment. Typical signaling molecules known as biomarkers identify abnormalities in cellular activity and serve as prognostic and diagnostic indicators. Biomarkers show great promise in clinical decision making, early and quick diagnosis, recurrence of illness, and tracking the effectiveness of cancer treatments. This review provides an overview of biomarkers, their benefits, and future directions for those new to the field of biomarker research in LC therapy.

Geographic Variation in Epigenetic Responses to Hypoxia in Deer Mice (Peromyscus maniculatus) Distributed Along an Elevational Gradient

Lowland and highland Peromyscus maniculatus populations display divergent, locally adapted physiological phenotypes shaped by altitudinal differences in oxygen availability. Many physiological responses to hypoxia seem to have evolved in lowland ancestors to offset episodic and localised bouts of low internal oxygen availability. However, upon chronic hypoxia exposure at high elevation, these responses can lead to physiological complications. Therefore, highland ancestry is often associated with evolved hypoxia responses, particularly traits promoting tolerance of constant hypoxia. Environmentally induced DNA methylation can dynamically alter gene expression patterns, providing a proximate basis for phenotypic plasticity. Given each population's differential reliance on plasticity for hypoxia tolerance, we hypothesised that lowland mice have a more robust epigenetic response to hypoxia exposure, driving trait plasticity, than highland mice. Using DNA methylation data of tissues from the heart's left ventricle, we show that upon hypoxia exposure, lowland mice chemically modulate the epigenetic landscape to a greater extent than highland mice, especially at key hypoxia-relevant genes such as Egln3. This gene is a regulator of the gene Epas1 that is frequently targeted for positive selection at high elevation. We find higher methylation among wild highland mice at gene Egln3 compared to wild lowland mice, suggesting a shared epigenetic ancestral response to episodic and chronic hypoxia. These findings highlight each population's distinct reliance on molecular plasticity driven by their unique evolutionary histories.

Quantum Mechanics/Molecular Mechanics Studies on the Excited-State Relaxation Mechanisms of Cytidine Analogues: 2'-Deoxy-5-Methylcytidine and 2'-Deoxy-5-Hydroxymethylcytidine in Aqueous Solution

We have used the high-level QM(CASPT2//CASSCF)/MM method to investigate the excited-state properties and decay pathways of two important cytidine analogues, i.e., 2'-deoxy-5-methylcytidine (5mdCyd) and 2'-deoxy-5-hydroxymethylcytidine (5hmdCyd), in aqueous solution. In view of the computed minimum-energy structures, conical intersections, and crossing points, and the relevant excited-state decay paths including the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the S1, T1, T2, and S0 states, we finally provided the feasible excited-state relaxation mechanisms of these two important epigenetic DNA nucleosides. Upon 285 nm photoexcitation, the lowest spectroscopically bright S1(ππ*) state is initially populated in the Franck-Condon (FC) region in both solvated systems and then mainly occurs direct IC to the ground state through the nearby accessible S1/S0 conical intersection, with the QM(CASPT2)/MM computed energy barriers of 9.5 and 1.6 kcal/mol for 5mdCyd and 5hmdCyd, respectively. In addition, the S1(ππ*) state can partially hop to the T1(ππ*) state directly or is mediated by the T2(ππ*) state. In comparison to the favorable singlet-mediated IC channel, the minor S1→T1 and S1→T2→T1 ISCs would take place slowly. Subsequently, the T1 state will further approach the nearby T1/S0 crossing point to slowly deactivate to the S0 state. Due to the T1/S0 crossing point above the T1-MIN as well with the small T1/S0 SOC, i.e., 9.8 kcal/mol and 0.3 cm-1 in 5mdCyd and 8.7 kcal/mol and 1.9 cm-1 in 5hmdCyd, the slow ISC would trap the system in the T1 state for a long time. The present work rationalizes the excited-state dynamics of 5mdCyd and 5hmdCyd in aqueous solution and could provide mechanistic insights into understanding the photophysics and photochemistry of similar epigenetic DNA nucleosides and their derivatives.

Quantum mechanics/molecular mechanics studies on mechanistic photophysics of epigenetic C5-halogenated DNA nucleosides: 2'-deoxy-5-chlorocytidine and 2'-deoxy-5-bromocytidine in aqueous solution

In this work, we have employed the high-level QM(CASPT2//CASSCF)/MM method to study the photophysical mechanisms of two important metabolized DNA/RNA nucleoside byproducts, i.e., 2'-deoxy-5-chlorocytidine (5CldCyd) and 2'-deoxy-5-bromocytidine (5BrdCyd), in aqueous solution. On the basis of our optimized minimum-energy structures, conical intersections, and crossing points, as well as the computed associated excited-state relaxation pathways involving the different internal conversion (IC) and intersystem crossing (ISC) processes in and between the S1, T1, T2, and S0 states, we have suggested the feasible excited-state relaxation mechanisms of these two important epigenetic halogenated DNA nucleosides. The initially populated spectroscopic bright 1ππ* state in the Franck-Condon (FC) region is the S1 state both for 5CldCyd and 5BrdCyd under 295 nm irradiation. The excited S1 state first evolves into its minimum S1-MIN and rapidly undergoes efficient IC to the S0 state via the nearby low-lying S1/S0 conical intersection. The corresponding energy barrier of the S1 → S0 IC path in 5CldCyd is estimated to be 4.6 kcal mol-1 at the QM(CASPT2)/MM level, while it is found to be an almost barrierless process in 5BrdCyd. In addition to this very efficient IC, the S1 state can partially slowly undergo ISC to transfer to the T1 state. Because the small spin-orbit couplings (SOCs) of S1/T1 and S1/T2 are estimated to be less than 5.0 cm-1 at the QM(CASPT2)/MM level, the ISC involved T1 formation is not so efficient. The resulting T1 state from the minor S1 → T1 and S1 → T2 → T1 ISCs will first relax to its minimum T1-MIN and continue to approach the nearby accessible T1/S0 crossing point, followed by further T1 → S0 ISC to the S0 state. Relatively, the T1 → S0 ISC of 5BrdCyd is significantly enhanced by a large T1/S0 SOC of 32.9 cm-1 at the T1/S0 crossing point. The present work rationalizes the excited-state dynamics of 5CldCyd and 5BrdCyd in aqueous solution and could provide mechanistic insights into understanding the photophysics of similar halogenated DNA nucleosides and their derivatives.

Molecular antiviral responses, immune priming and inheritance in insects

Viral diseases transmitted by insects to plants cause severe agricultural damage and arboviruses transmitted to humans cause severe disease outbreaks. The interaction between viruses and the insect defences is complex and has evolved into acting-counteracting molecular interplays. Viruses depict complex molecular mechanisms to ensure invasion, replication and exit the insect host cell, to invade other cells. On the other hand, insect cells use molecular strategies to recognize, halt replication and eliminate the invaders. In turn, virus counteract with evasive strategies. The main antiviral defence mechanism RNA interference (RNAi) recognizes and degrades viral RNA, thereby inhibiting viral replication. These in conjunction with other canonical immune pathways, Toll, IMD, JAK/STAT and Akt-ERK developed mainly to combat bacteria, fungi and protozoa, along with mechanisms to eliminate infected cells like apoptosis and phagocytosis comprise a multifactorial system. Insects exposed to an attenuated or sublethal viral infection could respond with faster and enhanced immune responses to the same pathogen (priming), which is like immunological memory in vertebrates. Several mechanisms have been proposed to explain priming, including endoreplication, epigenetic gene modifications by DNA methylation and histone acetylation. Priming could be inherited by the offspring (transgenerational immune priming, TGIP). However, the precise molecular mechanisms underlying TGIP remain to be elucidated. This article reviews the molecular mechanisms employed by insects to combat viral infections, discusses the current information and the outstanding research questions in the area.

Genome-wide DNA methylation patterns in Daphnia magna are not significantly associated with age

BACKGROUND

DNA methylation plays a crucial role in gene regulation and epigenetic inheritance across diverse organisms. Daphnia magna, a model organism in ecological and evolutionary research, has been widely used to study environmental responses, pharmaceutical toxicity, and developmental plasticity. However, its DNA methylation landscape and age-related epigenetic changes remain incompletely understood.

RESULTS

In this study, we characterized DNA methyltransferases (DNMTs) and mapped DNA methylation across the D. magna genome using whole-genome bisulfite sequencing. Our analysis identified three DNMTs: a highly expressed but nonfunctional de novo methyltransferase (DNMT3.1), alongside lowly expressed yet functional de novo methyltransferase (DNMT3.2) and maintenance methyltransferase (DNMT1). D. magna exhibits overall low DNA methylation, targeting primarily CpG dinucleotides. Methylation is sparse at promoters but elevated in the first exons downstream of transcription start sites, with these exons showing hypermethylation relative to adjacent introns. To examine age-associated DNA methylation changes, we analyzed D. magna individuals across multiple life stages. Our results showed no significant global differences in DNA methylation levels between young, mature, and old individuals, nor any age-related clustering in dimensionality reduction analyses. Attempts to construct an epigenetic clock using machine learning models did not yield accurate age predictions, likely due to the overall low DNA methylation levels and lack of robust age-associated methylation changes.

CONCLUSIONS

This study provides a comprehensive characterization of D. magna's DNA methylation landscape and DNMT enzymes, highlighting a distinct pattern of exon-biased CpG methylation. Contrary to prior studies, we found no strong evidence supporting age-associated epigenetic changes, suggesting that DNA methylation may have a limited role in aging in D. magna. These findings enhance our understanding of invertebrate epigenetics and emphasize the need for further research into the interplay between DNA methylation, environmental factors, and gene regulation in D. magna.

The DNA methylation landscape of primary triple-negative breast cancer

Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two epigenetic subtypes corresponding to a Basal and a non-Basal group, in which characteristic transcriptional patterns are correlated with DNA methylation of distal regulatory elements and epigenetic regulation of key steroid response genes and developmental transcription factors. Further subdivision of the Basal and non-Basal subtypes identifies subgroups transcending genetic and proposed TNBC mRNA subtypes, demonstrating widely differing immunological microenvironments, putative epigenetically-mediated immune evasion strategies, and a specific metabolic gene network in older patients that may be epigenetically regulated. Our study attempts to target the epigenetic backbone of TNBC, an approach that may inform future studies regarding tumor origins and the role of the microenvironment in shaping the cancer epigenome.

Comparative genome analysis and global methylation patterns for epigenetic study in the brackish water flea Diaphanosoma celebensis

The brackish water flea Diaphanosoma celebensis is a crucial organism in brackish and estuarine ecosystems, acting as a key trophic link between primary producers and higher trophic levels. Its small size, short life cycle, and high reproductive capacity make it an ideal model for studying ecological responses to environmental stressors, especially in polluted environments. This study provides a chromosome-level genome assembly of D. celebensis, consisting of 22 chromosomes with an N50 of 4,113,329 base pairs and 95.1 % completeness, achieved by combining de novo assembly with Hi-C data from D. dubium. Whole-genome bisulfite sequencing (WGBS) revealed distinct DNA methylation patterns, with exons showing higher methylation than introns and intergenic regions. A detailed analysis identified four gene clusters based on methylation levels. Cluster δ (highly methylated), enriched for pathways related to protein processing, ribosomal activity, and ubiquitin-mediated proteolysis, suggests a regulatory mechanism for stress adaptation in D. celebensis. In contrast, cluster α (hypo methylated), associated with transcription regulation and neural functions, highlights genes involved in cellular processes that may respond dynamically to environmental changes. Functional gene comparisons indicated significant differences in pathways related to ion transport and ubiquitination, emphasizing the unique adaptations of D. celebensis to its brackish environment. These findings provide a deeper understanding of the species' genomic and epigenetic regulation, offering valuable insights for future studies on its adaptation to environmental pollutants.

Variable performance of widely used bisulfite sequencing methods and read mapping software for DNA methylation

DNA methylation (DNAm) is the most commonly studied marker in ecological epigenetics, yet the performance of popular library preparation strategies and bioinformatic tools is seldom assessed and compared in genetically variable natural populations. We profiled DNAm using reduced representation bisulfite sequencing (RRBS) and whole genome bisulfite sequencing (WGBS), including technical and biological replicates from lab-reared and wild-caught threespine stickleback (Gasterosteus aculeatus). We then compared how the most commonly used read mapper and methylation caller (Bismark) performed relative to two alternative pipelines (BWA mem or BWA meth read mappers analyzed with MethyDackel). BWA meth provided 50% higher mapping efficiency than BWA mem and 45% higher efficiency than Bismark. Despite differences in mapping efficiency, BWA meth and Bismark produced highly similar methylation profiles, while BWA mem systematically discarded unmethylated cytosines. Sequencing depth filters had large impacts on CpG sites recovered across multiple individuals, with the largest impact on WGBS data. Notably, the prevalence of CpG sites with intermediate methylation levels is greatly reduced in RRBS data compared to WGBS, which may have important consequences for functional interpretations. We conclude by discussing how library construction and bisulfite alignment wrappers can influence SNP filtering, genomic coverage, and the abundance and reliability of data available for downstream analysis. Our analyses suggest that researchers studying genetically variable populations may prioritize filtering SNPs by constructing RRBS libraries with small insert sizes and paired end reads, which is counter to conventional wisdom.

Neural stem cell heterogeneity in adult hippocampus

Adult neurogenesis is a unique cellular process of the ongoing generation of new neurons throughout life, which primarily occurs in the subgranular zone (SGZ) of the dentate gyrus (DG) and the subventricular zone (SVZ) of the lateral ventricle. In the adult DG, newly generated granule cells from neural stem cells (NSCs) integrate into existing neural circuits, significantly contributing to cognitive functions, particularly learning and memory. Recently, more and more studies have shown that rather than being a homogeneous population of identical cells, adult NSCs are composed of multiple subpopulations that differ in their morphology and function. In this study, we provide an overview of the origin, regional characteristics, prototypical morphology, and molecular factors that contribute to NSC heterogeneity. In particular, we discuss the molecular mechanisms underlying the balance between activation and quiescence of NSCs. In summary, this review highlights that deciphering NSC heterogeneity in the adult brain is a challenging but critical step in advancing our understanding of tissue-specific stem cells and the process of neurogenesis in the adult brain.

Blood-Based DNA Methylation Biomarkers to Identify Risk and Progression of Cardiovascular Disease

Non-communicable diseases (NCDs) are the leading cause of death worldwide, with cardiovascular disease (CVD) accounting for half of all NCD-related deaths. The biological onset of CVD may occur long before the development of clinical symptoms, hence the urgent need to understand the molecular alterations underpinning CVD, which would facilitate intervention strategies to prevent or delay the onset of the disease. There is evidence to suggest that CVD develops through a complex interplay between genetic, lifestyle, and environmental factors. Epigenetic modifications, including DNA methylation, serve as proxies linking genetics and the environment to phenotypes and diseases. In the past decade, a growing list of studies has implicated DNA methylation in the early events of CVD pathogenesis. In this regard, screening for these epigenetic marks in asymptomatic individuals may assist in the early detection of CVD and serve to predict the response to therapeutic interventions. This review discusses the current literature on the relationship between blood-based DNA methylation alterations and CVD in humans. We highlight a set of differentially methylated genes that show promise as candidates for diagnostic and prognostic CVD biomarkers, which should be prioritized and replicated in future studies across additional populations. Finally, we discuss key limitations in DNA methylation studies, including genetic diversity, interpatient variability, cellular heterogeneity, study confounders, different methodological approaches used to isolate and measure DNA methylation, sample sizes, and cross-sectional study design.

The interplay between epigenomic and transcriptomic variation during ecotype divergence in stickleback

BACKGROUND

Populations colonizing contrasting environments are likely to undergo adaptive divergence and evolve ecotypes with locally adapted phenotypes. While diverse molecular mechanisms underlying ecotype divergence have been identified, less is known about their interplay and degree of divergence.

RESULTS

Here we integrated epigenomic and transcriptomic data to explore the interactions among gene expression, alternative splicing, DNA methylation, and microRNA expression to gauge the extent to which patterns of divergence at the four molecular levels are aligned in a case of postglacial divergence between marine and freshwater ecotypes of nine-spined sticklebacks (Pungitius pungitius). Despite significant genome-wide associations between epigenomic and transcriptomic variation, we found largely non-parallel patterns of ecotype divergence across epigenomic and transcriptomic levels, with predominantly nonoverlapping (ranging from 43.40 to 87.98%) sets of differentially expressed, spliced and methylated genes, and candidate genes targeted by differentially expressed miRNA between the ecotypes. Furthermore, we found significant variation in the extent of ecotype divergence across different molecular mechanisms, with differential methylation and differential splicing showing the highest and lowest extent of divergence between ecotypes, respectively. Finally, we found a significant enrichment of genes associated with ecotype divergence in differential methylation.

CONCLUSIONS

Our results suggest a nuanced relationship between epigenomic and transcriptomic processes, with alignment at the genome-wide level masking relatively independent effects of different molecular mechanisms on ecotype divergence at the gene level.

The landscape of cell lineage tracing

Cell fate changes play a crucial role in the processes of natural development, disease progression, and the efficacy of therapeutic interventions. The definition of the various types of cell fate changes, including cell expansion, differentiation, transdifferentiation, dedifferentiation, reprogramming, and state transitions, represents a complex and evolving field of research known as cell lineage tracing. This review will systematically introduce the research history and progress in this field, which can be broadly divided into two parts: prospective tracing and retrospective tracing. The initial section encompasses an array of methodologies pertaining to isotope labeling, transient fluorescent tracers, non-fluorescent transient tracers, non-fluorescent genetic markers, fluorescent protein, genetic marker delivery, genetic recombination, exogenous DNA barcodes, CRISPR-Cas9 mediated DNA barcodes, and base editor-mediated DNA barcodes. The second part of the review covers genetic mosaicism, genomic DNA alteration, TCR/BCR, DNA methylation, and mitochondrial DNA mutation. In the final section, we will address the principal challenges and prospective avenues of enquiry in the field of cell lineage tracing, with a particular focus on the sequencing techniques and mathematical models pertinent to single-cell genetic lineage tracing, and the value of pursuing a more comprehensive investigation at both the spatial and temporal levels in the study of cell lineage tracing.

Unveiling the Mechanisms of Pain in Endometriosis: Comprehensive Analysis of Inflammatory Sensitization and Therapeutic Potential

Endometriosis is a complicated, estrogen-dependent gynecological condition with a high morbidity rate. Pain, as the most common clinical symptom of endometriosis, severely affects women's physical and mental health and exacerbates socioeconomic burden. However, the specific mechanisms behind the occurrence of endometriosis-related pain remain unclear. It is currently believed that the occurrence of endometriosis pain is related to various factors, such as immune abnormalities, endocrine disorders, the brain-gut axis, angiogenesis, and mechanical stimulation. These factors induce systemic chronic inflammation, which stimulates the nerves and subsequently alters neural plasticity, leading to nociceptive sensitization and thereby causing chronic pain. In this paper, we compile and review the articles published on the study of nociceptive sensitization and endometriosis pain mechanisms. Starting from the factors influencing the chronic pain associated with endometriosis, we explain the relationship between these factors and chronic inflammation and further elaborate on the potential mechanisms by which chronic inflammation induces nociceptive sensitization. We aim to reveal the possible mechanisms of endometriosis pain, as well as nociceptive sensitization, and offer potential new targets for the treatment of endometriosis pain.

Nutraceutical Potential and Food Safety of Fructose in Soda and Diet Beverages

Fructose has been considered as an additive from soda beverages. For the approval of new additives or to extend the usage of an approved one, it is necessary to conduct toxicological studies in order to evaluate the DNA damage induced by these compounds. Our study is based on evaluating the safety and the nutraceutical potential of Fructose (FRU), a soda cola beverage (Pepsi-cola, PEP), and a diet soda cola (Diet Coke, DCC), characterizing the DNA changes induced in the Drosophila melanogaster organism model and in the human leukemia HL-60 cells performing different assays. Our results showed neither the toxicity nor mutagenic activity of FRU, PEP, and DCC in Drosophila melanogaster, while only PEP exhibited protective effects in the antitoxity assay, showing an 80% survival rate in combined treatments. FRU, but not PEP, enhanced lifespan parameters by up to 23 more days at the 5 mg/mL concentration. All three substances exhibited chemopreventive properties in some of the checkpoints carried out related to clastogenicity and methylation patterns in HL-60 cells. In conclusion, the tested compounds were safe at tested concentrations in Drosophila and showed moderate chemopreventive activity.

DNA methylation as a contributor to dysregulation of STX6 and other frontotemporal lobar degeneration genetic risk-associated loci

Frontotemporal Lobar Degeneration (FTLD) represents a spectrum of clinically, genetically, and pathologically heterogeneous neurodegenerative disorders characterised by progressive atrophy of the frontal and temporal lobes of the brain. The two major FTLD pathological subgroups are FTLD-TDP and FTLD-tau. While the majority of FTLD cases are sporadic, heterogeneity also exists within the familial cases, typically involving mutations in MAPT, GRN or C9orf72, which is not fully explained by known genetic mechanisms. We sought to address this gap by investigating the effect of epigenetic modifications, specifically DNA methylation variation, on genes associated with FTLD genetic risk in different FTLD subtypes. We compiled a list of genes associated with genetic risk of FTLD using text-mining databases and literature searches. Frontal cortex DNA methylation profiles were derived from three FTLD datasets containing different subgroups of FTLD-TDP and FTLD-tau: FTLD1m (N = 23) containing FTLD-TDP type A C9orf72 mutation carriers and TDP Type C sporadic cases, FTLD2m (N = 48) containing FTLD-Tau MAPT mutation carriers, FTLD-TDP Type A GRN mutation carriers, and FTLD-TDP Type B C9orf72 mutation carriers and FTLD3m (N = 163) progressive supranuclear palsy (PSP) cases, and corresponding controls. To investigate the downstream effects of DNA methylation further, we then leveraged transcriptomic and proteomic datasets for FTLD cases and controls to examine gene and protein expression levels. Our analysis revealed shared promoter region hypomethylation in STX6 across FTLD-TDP and FTLD-tau subtypes, though the largest effect size was observed in the PSP cases compared to controls (delta-beta = -32%, adjusted-p value=0.002). We also observed dysregulation of the STX6 gene and protein expression across FTLD subtypes. Additionally, we performed a detailed examination of MAPT, GRN and C9orf72 in subtypes with and without the presence of the genetic mutations and observed nominally significant differentially methylated CpGs in variable positions across the genes, often with unique patterns and downstream consequences in gene/protein expression in mutation carriers. We highlight the contribution of DNA methylation at different gene regions in regulating the expression of genes previously associated with genetic risk of FTLD, including STX6. We analysed the relationship of subtypes and presence of mutations with this epigenetic mechanism to increase our understanding of how these mechanisms interact in FTLD.

Epigenetic modifications in bladder cancer: crosstalk between DNA methylation and miRNAs

Bladder cancer (BC) is a malignant tumor characterized by a high incidence of urinary system diseases. The complex pathogenesis of BC has long been a focal point in medical research. With the robust development of epigenetics, the crucial role of epigenetic modifications in the occurrence and progression of BC has been elucidated. These modifications not only affect gene expression but also impact critical biological behaviors of tumor cells, including proliferation, differentiation, apoptosis, invasion, and metastasis. Notably, DNA methylation, an important epigenetic regulatory mechanism, often manifests as global hypomethylation or hypermethylation of specific gene promoter regions in BC. Alterations in this methylation pattern can lead to increased genomic instability, which profoundly influences the expression of proto-oncogenes and tumor suppressor genes. MiRNAs, as noncoding small RNAs, participate in various biological processes of BC by regulating target genes. Consequently, this work aims to explore the interaction mechanisms between DNA methylation and miRNAs in the occurrence and development of BC. Research has demonstrated that DNA methylation not only directly influences the expression of miRNA genes but also indirectly affects the maturation and functionality of miRNAs by modulating the methylation status of miRNA promoter regions. Simultaneously, miRNAs can regulate DNA methylation levels by targeting key enzymes such as DNA methyltransferases (DNMTs), thereby establishing a complex feedback regulatory network. A deeper understanding of the crosstalk mechanisms between DNA methylation and miRNAs in BC will contribute to elucidating the complexity and dynamics of epigenetic modifications in this disease, and may provide new molecular targets and strategies for the early diagnosis, treatment, and prognostic evaluation of BC.

Dnmt3b deficiency in adipocyte progenitor cells ameliorates obesity in female mice

Obesity arises from chronic energy imbalance where energy intake exceeds energy expenditure. Emerging evidence supports a key role of DNA methylation in the regulation of adipose tissue development and metabolism. We recently discovered a key role of DNA methylation, catalyzed by DNA methyltransferase 1 or 3a (Dnmt1 or 3a), in the regulation of adipocyte differentiation and metabolism. Here, we aimed to investigate the role of adipocyte progenitor cell Dnmt3b, an enzyme mediating de novo DNA methylation, in energy metabolism and obesity. We generated a genetic model with Dnmt3b knockout in adipocyte progenitor cells (PD3bKO) by crossing Dnmt3b -floxed mice with platelet-derived growth factor receptor alpha (Pdgfrα)-Cre mice. Dnmt3b gene deletion in adipocyte progenitors enhanced thermogenic gene expression in brown adipose tissue, increased overall energy expenditure, and mitigated high-fat diet (HFD)-induced obesity in female mice. PD3bKO mice also displayed a lower respiratory exchange ratio (RER), indicative of a metabolic shift favoring fat utilization as an energy source. Furthermore, female PD3bKO mice exhibited improved insulin sensitivity alongside their lean phenotype. In contrast, male PD3bKO mice showed no changes in body weight but demonstrated decreased insulin sensitivity, revealing a sexually dimorphic metabolic response to Dnmt3b deletion in adipocyte progenitor cells. These findings underscore the critical role of Dnmt3b in regulating energy homeostasis, body weight, and metabolic health, with significant implications for understanding sex-specific mechanisms of obesity and metabolism.

Xist RNA Dependent and Independent Mechanisms Regulate Dynamic X Chromosome Inactivation in B Lymphocytes

X-Chromosome Inactivation (XCI) involves epigenetic pathways to equalize X-linked gene expression between female and male mammals. XCI is dynamic in female B cells, as cytological enrichment of Xist RNA and heterochromatic marks on the inactive X-chromosome (Xi) are absent in naïve B cells yet return following mitogenic stimulation. Here, we asked whether any heterochromatic histone marks are present on the Xi in naïve B cells, and whether Xist RNA is required for their deposition and retention following stimulation. We find that the Xi in naïve B cells is depleted for H2AK119Ub and H3K9me3 but enriched for DNA methylation and H3K27me3, which maintain an Xist RNA-dependent epigenetic memory of XCI. Upon stimulation, Xist-independent H3K27me3 and Xist-dependent H2AK119Ub modifications accumulate across the Xi with temporal and spatial specificity. Our findings reveal the importance of Xist RNA, H3K27me3, and H2AK119Ub marks for the epigenetic integrity of X-linked genes across the Xi following female B cell stimulation.

Label-Free Surface-Enhanced Raman Scattering for Genomic DNA Cytosine Methylation Reading

DNA methylation has been widely studied with the goal of correlating the genome profiles of various diseases with epigenetic mechanisms. Multiple approaches have been developed that employ extensive steps, such as bisulfite treatments, polymerase chain reactions (PCR), restriction digestion, sequencing, mass analysis, etc., to identify DNA methylation. In this article, we report a facile label-free surface-enhanced Raman scattering (SERS) spectroscopy system that utilizes gold nanoparticles (AuNPs) for signal enhancement of methylated DNA. The key innovation of this work is to use anionic nanoparticles at a high ionic strength to introduce the aggregation of AuNPs with anionic DNA. When target methylated DNA is present, the presence of a methyl group in the cytosine C5 position of CpG sites induces a Raman peak at 1350 cm-1. Our amplification-free system has a limit of detection (LOD) of 5% and a limit of quantification (LOQ) of 16% with good specificity. The method was applied to determine the hypermethylated levels of the germline of colorectal cancer cell lines SW48 and SW480. Our simple label-free method holds the potential to read the disease-associated methylation of genomic DNA.

Epigenetic Mechanisms in Osteoporosis: Exploring the Power of m6A RNA Modification

Osteoporosis, recognised as a metabolic disorder, has emerged as a significant burden on global health. Although available treatments have made considerable advancements, they remain inadequately addressed. In recent years, the role of epigenetic mechanisms in skeletal disorders has garnered substantial attention, particularly concerning m6A RNA modification. m6A is the most prevalent dynamic and reversible modification in eukaryotes, mediating various metabolic processes of mRNAs, including splicing, structural conversion, translation, translocation and degradation and serves as a crucial component of epigenetic modification. Research has increasingly validated that m6A plays a vital role in the proliferation, differentiation, migration, invasion,and repair of bone marrow mesenchymal stem cells (BMSCs), osteoblasts and osteoclasts, all of which impact the whole process of osteoporosis pathogenesis. Continuous efforts have been made to target m6A regulators and natural products derived from traditional medicine, which exhibit multiple biological activities such as anti-inflammatory and anticancer effects, have emerged as a valuable resources for m6A drug discovery. This paper elaborates on m6A methylation and its regulatory role in osteoporosis, emphasising its implications for diagnosis and treatment, thereby providing theoretical references.

Targeting the epigenome with advanced delivery strategies for epigenetic modulators

Epigenetics mechanisms play a significant role in human diseases by altering DNA methylation status, chromatin structure, and/or modifying histone proteins. By modulating the epigenetic status, the expression of genes can be regulated without any change in the DNA sequence itself. Epigenetic drugs exhibit promising therapeutic efficacy against several epigenetically originated diseases including several cancers, neurodegenerative diseases, metabolic disorders, cardiovascular disorders, and so forth. Currently, a considerable amount of research is focused on discovering new drug molecules to combat the existing research gap in epigenetic drug therapy. A novel and efficient delivery system can be established as a promising approach to overcome the drawbacks associated with the current epigenetic modulators. Therefore, formulating the existing epigenetic drugs with distinct encapsulation strategies in nanocarriers, including solid lipid nanoparticles, nanogels, bio-engineered nanocarriers, liposomes, surface modified nanoparticles, and polymer-drug conjugates have been examined for therapeutic efficacy. Nonetheless, several epigenetic modulators are untouched for their therapeutic potential through different delivery strategies. This review provides a comprehensive up to date discussion on the research findings of various epigenetics mechanism, epigenetic modulators, and delivery strategies utilized to improve their therapeutic outcome. Furthermore, this review also highlights the recently emerged CRISPR tool for epigenome editing.

DNA methylation in mammalian development and disease

The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.

Targeting protein tyrosine phosphatase non-receptor type 6 (PTPN6) as a therapeutic strategy in acute myeloid leukemia

Acute myeloid leukemia (AML) is a heterogeneous hematologic malignancy characterized by the clonal expansion of myeloid progenitor cells. Despite advancements in treatment, the prognosis for AML patients remains poor, highlighting the need for novel therapeutic targets. Protein Tyrosine Phosphatase Non-Receptor Type 6 (PTPN6), also known as SHP-1, is a critical regulator of hematopoietic cell signaling and has been implicated in various leukemias. This study investigates the therapeutic potential of targeting PTPN6 in AML. We employed both in vitro and in vivo models to evaluate the effects of PTPN6 inhibition on AML cell proliferation, apoptosis, and differentiation. Our results demonstrate that PTPN6 inhibition leads to a significant reduction in AML cell viability, induces apoptosis, and promotes differentiation of leukemic cells into mature myeloid cells. Mechanistic studies revealed that PTPN6 inhibition disrupts key signaling pathways involved in AML pathogenesis, including the JAK/STAT and PI3K/AKT pathways. Furthermore, the combination of PTPN6 inhibitors with standard chemotherapeutic agents exhibited a synergistic effect, enhancing the overall therapeutic efficacy. These findings suggest that PTPN6 is a promising therapeutic target in AML and warrants further investigation into the development of PTPN6 inhibitors for clinical application in AML treatment.

Exposure to a Titanium Dioxide Product Alters DNA Methylation in Human Cells

The safety of titanium dioxide (TiO2), widely used in foods and personal care products, has been of ongoing concern. Significant toxicity of TiO2 has been reported, suggesting a risk to human health. To evaluate its potential epigenotoxicity, the effect of exposure to a TiO2 product to which humans could be exposed on DNA methylation, a primary epigenetic mechanism, was investigated using two human cell lines (Caco-2 (colorectal) and HepG2 (liver)) relevant to human exposure. Global methylation was determined by enzyme-linked immunosorbent assay-based immunochemical analysis. Gene promoter methylation was evaluated using EpiTect Methyl II Signature PCR System Array technology. Expression of DNA methyltransferases, MBD2, and URHF1 was quantified by qRT-PCR. A decrease in global DNA methylation was observed in both cell lines. Across the cell lines, seven genes (BNIP3, DNAJC15, GADD45G, GDF15, INSIG1, SCARA3, and TP53) were identified in which promoters were methylated. Changes in promoter methylation were associated with gene expression. Results also revealed aberrant expression of regulatory genes, DNA methyltransferases, MBD2, and UHRF1. Findings from the study clearly demonstrate the impact of TiO2 exposure on DNA methylation in two cell types, supporting the potential involvement of this epigenetic mechanism in its biological responses. Hence, epigenetic studies are critical for complete assessment of potential risk from exposure.

Suppressing the Aging Phenotype of Mesenchymal Stromal Cells: Are We Ready for Clinical Translation?

Mesenchymal stem/stromal cells (MSCs) are involved in the maintenance and regeneration of a large variety of tissues due to their stemness and multi-lineage differentiation capability. Harnessing these advantageous features, a flurry of clinical trials have focused on MSCs to treat different pathologies, but only few protocols have received regulatory approval so far. Among the various causes hindering MSCs' efficacy is the emergence of cellular senescence, which has been correlated with specific characteristics, such as morphological and epigenetic alterations, DNA damage, ROS production, mitochondrial dysfunction, telomere shortening, non-coding RNAs, loss of proteostasis, and a peculiar senescence-associated secretory phenotype. Several strategies have been investigated for delaying or even hopefully reverting the onset of senescence, as assessed by the senescent phenotype of MSCs. Here, the authors reviewed the most updated literature on the potential causes of senescence, with a particular emphasis on the current and future therapeutic approaches aimed at reverting senescence and/or extending the functional lifespan of stem cells.

In Vivo and In Vitro Studies Assessing the Safety of Monosodium Glutamate

The controversial results of research on monosodium glutamate demand a new data corpus for the overall safety evaluation. Both animal and cellular model systems have been used to add a multilevel scope on its biological effects. The Drosophila melanogaster animal model has been used to test a wide range of concentrations for safety purposes: toxicity, genotoxicity, longevity and health span. Medium concentrations corresponding to the human acceptable daily intake (ADI) (0.06 mg/mL) were not toxic nor genotoxic for Drosophila and safe for the lifespan parameters. Once safety was determined, the possible nutraceutical effects of monosodium glutamate was monitored in terms of antitoxicity, antigenotoxicity assays and health span. The results for protective activity against hydrogen peroxide were positive in terms of the medium concentration, antitoxic and antigenotoxic in terms of inhibiting the genotoxicity induced by the oxidative toxin up to 43.7% and increasing the health span expectancy by 32% in terms of days. Monosodium glutamate has been demonstrated to be cytotoxic against the model tumour cell line HL-60, not only in a necrotic way but through internucleosomal DNA fragmentation antitumour activity. The significant LINE1 DNA sequence methylation of HL-60 tumour cells induced by monosodium glutamate is a molecular marker for chemoprevention. Conclusions: the slight or non-significant positive nutraceutical and chemo preventive potential showed by monosodium glutamate at its ADI concentration can be considered as a safe dose for a moderate consumption.

The Genome Architecture of the Copepod Eurytemora carolleeae - the Highly Invasive Atlantic Clade of the Eurytemoraaffinis Species Complex

Copepods are among the most abundant organisms on the planet and play critical functions in aquatic ecosystems. Among copepods, populations of the Eurytemora affinis species complex are numerically dominant in many coastal habitats and serve as food sources for major fisheries. Intriguingly, certain populations possess the unusual capacity to invade novel salinities on rapid time scales. Despite their ecological importance, high-quality genomic resources have been absent for calanoid copepods, limiting our ability to comprehensively dissect the genome architecture underlying the highly invasive and adaptive capacity of certain populations. Here, we present the first chromosome-level genome of a calanoid copepod, from the Atlantic clade (Eurytemora carolleeae) of the E. affinis species complex. This genome was assembled using high-coverage PacBio long-read and Hi-C sequences of an inbred line, generated through 30 generations of full-sib mating. This genome, consisting of 529.3 Mb (contig N50 = 4.2 Mb, scaffold N50 = 140.6 Mb), was anchored onto four chromosomes. Genome annotation predicted 20,262 protein-coding genes, of which ion transport-related gene families were substantially expanded based on comparative analyses of 12 additional arthropod genomes. Also, we found genome-wide signatures of historical gene body methylation of the ion transport-related genes and the significant clustering of these genes on each chromosome. This genome represents one of the most contiguous copepod genomes to date and is among the highest quality marine invertebrate genomes. As such, this genome provides an invaluable resource to help yield fundamental insights into the ability of this copepod to adapt to rapidly changing environments.

Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows

Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. The analysis uncovered significant differences between cows resilient and susceptible to mastitis, with 196,275 differentially methylated cytosines (DMCs) and 1,227 Differentially Methylated Regions (DMRs). Key genes associated with the immune response and morphological traits, including ENOPH1, MYL10 and KIR2DL5A, were identified by our analysis. Quantitative trait loci (QTL) were also highlighted and the body weight trait was the most targeted by DMCs and DMRs. Based on our results, the risk of developing mastitis can potentially be estimated with as few as fifty methylation biomarkers, paving the way for early animal selection. This research sets the stage for improved animal health management and economic yields within the framework of agricultural sustainability through early selection based on the epigenetic status of animals.

Base-excision repair pathway shapes 5-methylcytosine deamination signatures in pan-cancer genomes

Transition of cytosine to thymine in CpG dinucleotides is the most frequent type of mutation in cancer. This increased mutability is commonly attributed to the spontaneous deamination of 5-methylcytosine (5mC), which is normally repaired by the base-excision repair (BER) pathway. However, the contribution of 5mC deamination in the increasing diversity of cancer mutational signatures remains poorly explored. We integrate mutational signatures analysis in a large series of tumor whole genomes with lineage-specific epigenomic data to draw a detailed view of 5mC deamination in cancer. We uncover tumor type-specific patterns of 5mC deamination signatures in CpG and non-CpG contexts. We demonstrate that the BER glycosylase MBD4 preferentially binds to active chromatin and early replicating DNA, which correlates with lower mutational burden in these domains. We validate our findings by modeling BER deficiencies in isogenic cell models. Here, we establish MBD4 as the main actor responsible for 5mC deamination repair in humans.

The Power of WNT5A and FZD3 Gene Expression and Methylation Status in the Diagnosis-Treatment-Cause Triangle in Tension-Type Headache

DNA methylation is the epigenetic pathway controlling cellular gene expression. Methylation is a natural and cellular epigenetic mechanism for gene silencing. The fact that the genes that the cell decides to be silent do not speak or begin to speak may coincide with diseases. For explanatory evidence, changes at the DNA level can provide realistic information. Wnt/β-catenin signaling has an important role in the pain process. For this purpose, we investigated the relationship between clinical data, wingless-type MMTV integration site family, member 5A (WNT5A), and Frizzled Class Receptor 3 (FZD3) gene methylation and expression in a cohort of tension-type headache (TTH) patients (N = 130) and healthy control (N = 117) individuals. Comorbidities were evaluated. Methylation profiling was performed using Real-Time PCR with a TaqMan primer-probe. The diagnostic power (receiver operating characteristic-ROC) was determined according to the expression and methylation status. Ultimately, WNT5A was found to be upregulated and hypermethylated, and FZD3 was found to be upregulated and hypomethylated. Finally, the area under the curve (AUC) data for FZD3 upregulation (0.983) and hypomethylation (0.866) showed diagnostic values. WNT5A and FZD3 may contribute to the pathogenesis of the disease depending on their expression and methylation profile during the TTH process. At the same time, diagnostic powers have the potential to be a resource for early treatment and new therapeutic approaches.

The genetics and hormonal basis of human gender identity

Gender identity refers to one's psychological sense of their own gender. Establishing gender identity is a complex phenomenon, and the diversity of gender expression challenges simplistic or unified explanations. For this reason, the extent to which it is determined by nature (biological) or nurture (social) is still debatable. The biological basis of gender identity cannot be modeled in animals and is best studied in people who identify with a gender that is different from the sex of their genitals such as transgender people and people with disorders/differences of sex development. Numerous research studies have delved into unraveling the intricate interplay of hormonal, neuroanatomic/neurofunctional, and genetic factors in the complex development of core gender identity. In this review, we explore and consolidate existing research that provides insights into the biological foundations of gender identity, enhancing our understanding of this intriguing human psychological trait.

LINE-1 cfDNA Methylation as an Emerging Biomarker in Solid Cancers

Epigenetic dysregulation is a hallmark of many human malignancies, with DNA methylation being a primary mechanism influencing gene expression and maintaining genomic stability. Genome-wide hypomethylation, characteristic of many cancers, is partly attributed to the demethylation of repetitive elements, including LINE-1, a prevalent non-LTR retrotransposon. The methylation status of LINE-1 is closely associated with overall genomic methylation levels in tumors. cfDNA comprises extracellular DNA fragments found in bodily fluids such as plasma, serum, and urine, offering a dynamic snapshot of the genetic and epigenetic landscape of tumors. This real-time sampling provides a minimally invasive avenue for cancer diagnostics, prognostics, and monitoring. The methylation status of LINE-1 in cfDNA has emerged as a promising biomarker, with several studies highlighting its potential in diagnosing and predicting outcomes in cancer patients. Recent research also suggests that cfDNA-based LINE-1 methylation analysis could serve as a valuable tool in evaluating the efficacy of cancer therapies, including immunotherapy. The growing clinical significance of cfDNA calls for a closer examination of its components, particularly repetitive elements like LINE-1. Despite their importance, the role of LINE-1 elements in cfDNA has not been thoroughly gauged. We aim to address this gap by reviewing the current literature on LINE-1 cfDNA assays, focusing on their potential applications in diagnostics and disease monitoring.

Aging drives a program of DNA methylation decay in plant organs

How organisms age is a question with broad implications for human health. In mammals, DNA methylation is a biomarker for biological age, which may predict age more accurately than date of birth. However, limitations in mammalian models make it difficult to identify mechanisms underpinning age-related DNA methylation changes. Here, we show that the short-lived model plant Arabidopsis thaliana exhibits a loss of epigenetic integrity during aging, causing heterochromatin DNA methylation decay and the expression of transposable elements. We show that the rate of epigenetic aging can be manipulated by extending or curtailing lifespan, and that shoot apical meristems are protected from this aging process. We demonstrate that a program of transcriptional repression suppresses DNA methylation maintenance pathways during aging, and that mutants of this mechanism display a complete absence of epigenetic decay. This presents a new paradigm in which a gene regulatory program sets the rate of epigenomic information loss during aging.

Determination of global DNA methylation level by methylation-sensitive comet assay in patients with urinary bladder cancer

DNA methylation is an important mechanism in the regulation of gene expression and maintenance of genomic integrity. Aberrant DNA methylation is an early event in carcinogenesis. DNA methyltransferase inhibitors are used to restore aberrant DNA methylation and inhibit tumor growth. Evaluation of DNA methylation level is important for an effective anti-cancer therapy. In the present study, the determination of global DNA methylation levels in patients with urinary bladder cancer was proposed. The methylation-sensitive comet assay determined the global DNA methylation level at the level of single cells. McrBC enzyme, a methylation-sensitive restriction endonuclease, was used for enzymatic digestion to generate additional breaks at methylated sites. % DNA methylation level was significantly higher in patients with bladder cancer compared to the control group. The clinical performance of % DNA methylation analysis by methylation-sensitive comet assay was evaluated by ROC curve. Using the cutoff value of 6.5% DNA methylation, 92% sensitivity, and 42% specificity were obtained. In conclusion, global DNA methylation measured by methylation-sensitive comet assay may be a promising noninvasive biomarker that reduces interventional tests required in the diagnosis and follow-up of urinary bladder cancer.

A review of environmental epigenetics in aquatic invertebrates

Aquatic ecosystems face significant challenges due to increasing human-induced environmental stressors. Recent studies emphasize the role of epigenetic mechanisms in the stress responses and adaptations of organisms to those stressors. Epigenetics influences gene expression, enabling phenotypic plasticity and transgenerational effects. Therefore, understanding the epigenetic responses of aquatic invertebrates to environmental stressors is imperative for aquatic ecosystem research. In this study, we organize the mechanisms of epigenetics in aquatic invertebrates and explore their roles in the responses of aquatic invertebrates to environmental stressors. Furthermore, we discuss the inheritance of epigenetic changes and their influence across generations in aquatic invertebrates. A comprehensive understanding of epigenetic responses is crucial for long-term ecosystem management and conservation strategies in the face of irreversible climate change in aquatic environments. In this review, we synthesize existing knowledge about environmental epigenetics in aquatic invertebrates to provide insights and suggest directions for future research.

Mediation of DNA methylation (cg04622888 and cg05037505) in the association between childhood maltreatment and non-suicidal self-injury in early adolescents

It is unclear whether DNA methylation underlies the association between childhood maltreatment (CM) and non-suicidal self-injury (NSSI) in early adolescents. We aim to explore the mediation of specific DNA methylation sites in the associations of CM and its subtypes with NSSI, following investigation on the association between specific DNA methylation sites and NSSI. A case-control study was conducted to examine 155 adolescents aged 12-14 years who were identified to have engaged in NSSI and 201 controls. CM and its subtypes were evaluated by using the Childhood Trauma Questionnaire. The EPIC 850 k Bead Chip was used to discover differential methylation sites (DMSs) in the peripheral blood between 10 NSSI cases and 10 controls. Targeted pyrosequencing was employed to detect the levels of specific DMSs among the total study population, which were selected based on bioinformatics analyses and literature review. We discovered 456 DMSs between NSSI cases and controls, 219 were hypermethylated and 237 were hypomethylated. After controlling for potential confounders, CM or its subtypes, and the methylation of cg04622888 and cg05037505 were all significantly associated with NSSI (all P < 0.05). The total association of CM and its subtypes with NSSI were all significantly (all P < 0.05), with the standardized coefficient (β) ranged from 0.12 for physical neglect to 0.24 for emotional neglect and CM. Significant indirect association of physical neglect with NSSI through methylation of cg04622888 was observed and the mediating proportion was 0.14 (95%CI 0.06-0.23). Significant indirect associations of emotional abuse, emotional neglect, and physical neglect with NSSI through methylation of cg05037505 were also observed, and the mediating proportions were 0.09 (95%CI 0.04-0.14), 0.08 (95%CI, 0.03-0.14) and 0.19 (95%CI 0.07-0.32), respectively. Data of this study suggested that methylation of cg04622888 and cg05037505 were independently associated with NSSI among early adolescents, and they partially mediated the associations of emotional abuse, emotional neglect, and physical abuse with NSSI.

Using human disease mutations to understand de novo DNA methyltransferase function

DNA methylation is a repressive epigenetic mark that is pervasive in mammalian genomes. It is deposited by DNA methyltransferase enzymes (DNMTs) that are canonically classified as having de novo (DNMT3A and DNMT3B) or maintenance (DNMT1) function. Mutations in DNMT3A and DNMT3B cause rare Mendelian diseases in humans and are cancer drivers. Mammalian DNMT3 methyltransferase activity is regulated by the non-catalytic region of the proteins which contain multiple chromatin reading domains responsible for DNMT3A and DNMT3B recruitment to the genome. Characterising disease-causing missense mutations has been central in dissecting the function and regulation of DNMT3A and DNMT3B. These observations have also motivated biochemical studies that provide the molecular details as to how human DNMT3A and DNMT3B mutations drive disorders. Here, we review progress in this area highlighting recent work that has begun dissecting the function of the disordered N-terminal regions of DNMT3A and DNMT3B. These studies have elucidated that the N-terminal regions of both proteins mediate novel chromatin recruitment pathways that are central in our understanding of human disease mechanisms. We also discuss how disease mutations affect DNMT3A and DNMT3B oligomerisation, a process that is poorly understood in the context of whole proteins in cells. This dissection of de novo DNMT function using disease-causing mutations provides a paradigm of how genetics and biochemistry can synergise to drive our understanding of the mechanisms through which chromatin misregulation causes human disease.

Role of sexually dimorphic oxytocin receptor-expressing neurons in the anteroventral periventricular nucleus on maternal behavior

Oxytocin is a neuropeptide produced by magnocellular neurosecretory neurons located primarily in the supraoptic nucleus and paraventricular nucleus of the hypothalamus. The long axons of these neurons project to the neurohypophysis where oxytocin is released into the general circulation in response to the physiological demands. Oxytocin plays critical roles in female reproductive physiology, specifically in uterine contraction during labor and milk ejection while nursing. Oxytocin is also called "the love hormone" due to its modulatory roles in prosocial behaviors, including social recognition, maternal behavior, and pair bonding. Oxytocin influences behaviors by binding to oxytocin receptors (OXTR) located in various parts of the brain. Previously, we discovered a group of estrogen-dependent OXTR neurons that is exclusively present in the anteroventral periventricular nucleus (AVPV) of females but not of males. The female-specific expression of OXTR in the AVPV is a rare case of neurochemically-demonstrated, all-or-none sexual dimorphism in the brain. In this review, the cellular characterization and functional significance of the sexually dimorphic OXTR neurons in the AVPV as well as the clinical implications of the research will be discussed.

Human 8-oxoguanine glycosylase OGG1 binds nucleosome at the dsDNA ends and the super-helical locations

The human glycosylase OGG1 extrudes and excises the oxidized DNA base 8-oxoguanine (8-oxoG) to initiate base excision repair and plays important roles in many pathological conditions such as cancer, inflammation, and neurodegenerative diseases. Previous structural studies have used a truncated protein and short linear DNA, so it has been unclear how full-length OGG1 operates on longer DNA or on nucleosomes. Here we report cryo-EM structures of human OGG1 bound to a 35-bp long DNA containing an 8-oxoG within an unmethylated Cp-8-oxoG dinucleotide as well as to a nucleosome with an 8-oxoG at super-helical location (SHL)-5. The 8-oxoG in the linear DNA is flipped out by OGG1, consistent with previous crystallographic findings with a 15-bp DNA. OGG1 preferentially binds near dsDNA ends at the nucleosomal entry/exit sites. Such preference may underlie the enzyme's function in DNA double-strand break repair. Unexpectedly, we find that OGG1 bends the nucleosomal entry DNA, flips an undamaged guanine, and binds to internal nucleosomal DNA sites such as SHL-5 and SHL+6. We suggest that the DNA base search mechanism by OGG1 may be chromatin context-dependent and that OGG1 may partner with chromatin remodelers to excise 8-oxoG at the nucleosomal internal sites.

Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors

Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of "resistance," or the capacity of a system to minimize change in response to a disturbance, and "recovery," or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.

Precision DNA methylation typing via hierarchical clustering of Nanopore current signals and attention-based neural network

Decoding DNA methylation sites through nanopore sequencing has emerged as a cutting-edge technology in the field of DNA methylation research, as it enables direct sequencing of native DNA molecules without the need for prior enzymatic or chemical treatments. During nanopore sequencing, methylation modifications on DNA bases cause changes in electrical current intensity. Therefore, constructing deep neural network models to decode the electrical signals of nanopore sequencing has become a crucial step in methylation site identification. In this study, we utilized nanopore sequencing data containing diverse DNA methylation types and motif sequence diversity. We proposed a feature encoding method based on current signal clustering and leveraged the powerful attention mechanism in the Transformer framework to construct the PoreFormer model for identifying DNA methylation sites in nanopore sequencing. The model demonstrated excellent performance under conditions of multi-class methylation and motif sequence diversity, offering new insights into related research fields.

Heat stress in symbiotic dinoflagellates: Implications on oxidative stress and cellular changes

Global warming has been shown to harmfully affect symbiosis between Symbiodiniaceae and other marine invertebrates. When symbiotic dinoflagellates (the genus Breviolum) were in vitro exposed to acute heat stress of +7 °C for a period of 5 days, the results revealed the negative impact on all physiological and other cellular parameters measured. Elevated temperatures resulted in a severe reduction in algal density of up to 9.5-fold, as well as pigment concentrations, indicating the status of the physiological stress and early signs of photo-bleaching. Reactive oxygen species (ROS) were increased in all heated dinoflagellate cells, while the antioxidant-reduced glutathione levels initially dropped on day one but increased under prolonged temperature stress. The cell viability parameters were reduced by 97 % over the heating period, with an increased proportion of apoptotic and necrotic cells. Autofluorescence (AF) for Cy5-PE 660-20 was reduced from 1.7-fold at day 1 to up to 50-fold drop at the end of heating time, indicating that the AF changes were highly sensitive to heat stress and that it could be an extremely sensitive tool for assessing the functionality of algal photosynthetic machinery. The addition of the drug 5-AZA-2'-deoxycytidine (5-AZA), which inhibits DNA methylation processes, was assessed in parallel and contributed to some alterations in algal cellular stress response. The presence of drug 5-AZA combined with the temperature stress had an additional impact on Symbiodiniaceae density and cell complexity, including the AF levels. These variations in cellular stress response under heat stress and compromised DNA methylation conditions may indicate the importance of this epigenetic mechanism for symbiotic dinoflagellate thermal tolerance adaptability over a longer period, which needs further exploration. Consequently, the increased ROS levels and changes in AF signals reported during ongoing heat stress in dinoflagellate cells could be used as early stress biomarkers in these microalgae and potentially other photosynthetic species.

Molecular mechanisms of avian immunoglobulin gene diversification and prospect for industrial applications

Poultry immunoglobulin genes undergo diversification through homologous recombination (HR) and somatic hypermutation (SHM). Most animals share a similar system in immunoglobulin diversification, with the rare exception that human and murine immunoglobulin genes diversify through V(D)J recombination. Poultry possesses only one functional variable gene for each immunoglobulin heavy (HC) and light chains (LC), with clusters of non-productive pseudogenes upstream. During the B cell development, the functional variable gene is overwritten by sequences from the pseudo-variable genes via a process known as gene conversion (GC), a kind of HR. Point mutations caused in the functional variable gene also contribute to immunoglobulin diversification. This review discusses the latest findings on the molecular mechanisms of antibody gene diversification in poultry, using chickens as a model. Additionally, it will outline how these basic research findings have recently been applied especially in the medical field.

Immune microenvironmental heterogeneity according to tumor DNA methylation phenotypes in microsatellite instability-high colorectal cancers

The detailed association between tumor DNA methylation, including CpG island methylation, and tumor immunity is poorly understood. CpG island methylator phenotype (CIMP) is observed typically in sporadic colorectal cancers (CRCs) with microsatellite instability-high (MSI-H). Here, we investigated the differential features of the tumor immune microenvironment according to CIMP status in MSI-H CRCs. CIMP-high (CIMP-H) or CIMP-low/negative (CIMP-L/0) status was determined using MethyLight assay in 133 MSI-H CRCs. All MSI-H CRCs were subjected to digital pathology-based quantification of CD3 + /CD8 + /CD4 + /FoxP3 + /CD68 + /CD204 + /CD177 + tumor-infiltrating immune cells using whole-slide immunohistochemistry. Programmed death-ligand 1 (PD-L1) immunohistochemistry was evaluated using the tumor proportion score (TPS) and combined positive score (CPS). Representative cases were analyzed using whole-exome and RNA-sequencing. In 133 MSI-H CRCs, significantly higher densities of CD8 + tumor-infiltrating lymphocytes (TILs) were observed in CIMP-H tumors compared with CIMP-L/0 tumors. PD-L1 TPS and CPS in CIMP-H tumors were higher than in CIMP-L/0 tumors. Next-generation sequencing revealed that, compared with CIMP-L/0 tumors, CIMP-H tumors had higher fractions of CD8 + T cells/cytotoxic lymphocytes, higher cytolytic activity scores, and activated immune-mediated cell killing pathways. In contrast to CIMP-L/0 tumors, most CIMP-H tumors were identified as consensus molecular subtype 1, an immunogenic transcriptomic subtype of CRC. However, there were no differences in tumor mutational burden (TMB) between CIMP-H and CIMP-L/0 tumors in MSI-H CRCs. In conclusion, CIMP-H is associated with abundant cytotoxic CD8 + TILs and PD-L1 overexpression independent of TMB in MSI-H CRCs, suggesting that CIMP-H tumors represent a typical immune-hot subtype and are optimal candidates for immunotherapy in MSI-H tumors.

Dietary Organic Zinc Supplementation Modifies the Oxidative Genes via RORγ and Epigenetic Regulations in the Ileum of Broiler Chickens Exposed to High-Temperature Stress

Heat stress (HS) is a significant concern in broiler chickens, which is vital for global meat supply in the dynamic field of poultry farming. The impact of heat stress on the ileum and its influence on the redox homeostatic genes in chickens remains unclear. We hypothesized that adding zinc to the feed of heat-stressed broilers would improve their resilience to heat stress. However, this study aimed to explore the effects of organic zinc supplementation under HS conditions on broiler chickens' intestinal histology and regulation of HS index genes. In this study, 512 Xueshan chickens were divided into four groups: vehicle, HS, 60 mg/kg zinc, and HS + 60 mg/kg zinc groups. Findings revealed that zinc supply positively increased the VH and VH: CD in the ileum of the broilers compared to the HS group, while CD and VW decreased in Zn and HS+Zn supplemented broilers. Zn administration significantly increased superoxide dismutase (SOD), catalase (CAT), glutathione (GSH), and decreased the enzymatic activities of reactive oxygen species (ROS) and malondialdehyde (MDA) compared to the HS group. In addition, Zn administration significantly increased relative ATP, complex I, III, and V enzyme activity compared to the HS group. Furthermore, the expression of acyl-CoA synthetase long-chain family member 4 (ACSL4), lactate transporter 3 (LPCAT3), peroxiredoxin (PRX), and transferrin receptor (TFRC) in the protein levels was extremely downregulated in HS+Zn compared to the HS group. Zn supply significantly decreased the enrichment of RORγ, P300, and SRC1 at target loci of ACSL4, LPCAT3, and PRX compared to the HS group. The occupancies of histone active marks H3K9ac, H3K18ac, H3K27ac, H3K4me1, and H3K18bhb at the locus of ACSL4 and LPCAT3 were significantly decreased in HS+Zn compared to the HS group. Moreover, H3K9la and H3K18la at the locus of ACSL4 and LPCAT3 were significantly decreased in HS+Zn compared to the HS group. This study emphasizes that organic Zn is a potential strategy for modulating the oxidative genes ACSL4, LPCAT3, PRX, and TFRC in the ileum of chickens via nuclear receptor RORγ regulation and histone modifications.

Epigenetics Research in Evolutionary Biology: Perspectives on Timescales and Mechanisms

Epigenetics research in evolutionary biology encompasses a variety of research areas, from regulation of gene expression to inheritance of environmentally mediated phenotypes. Such divergent research foci can occasionally render the umbrella term "epigenetics" ambiguous. Here I discuss several areas of contemporary epigenetics research in the context of evolutionary biology, aiming to provide balanced views across timescales and molecular mechanisms. The importance of epigenetics in development is now being assessed in many nonmodel species. These studies not only confirm the importance of epigenetic marks in developmental processes, but also highlight the significant diversity in epigenetic regulatory mechanisms across taxa. Further, these comparative epigenomic studies have begun to show promise toward enhancing our understanding of how regulatory programs evolve. A key property of epigenetic marks is that they can be inherited along mitotic cell lineages, and epigenetic differences that occur during early development can have lasting consequences on the organismal phenotypes. Thus, epigenetic marks may play roles in short-term (within an organism's lifetime or to the next generation) adaptation and phenotypic plasticity. However, the extent to which observed epigenetic variation occurs independently of genetic influences remains uncertain, due to the widespread impact of genetics on epigenetic variation and the limited availability of comprehensive (epi)genomic resources from most species. While epigenetic marks can be inherited independently of genetic sequences in some species, there is little evidence that such "transgenerational inheritance" is a general phenomenon. Rather, molecular mechanisms of epigenetic inheritance are highly variable between species.

Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1

Epigenetic factors are well-established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role of DNA methyltransferases (Dnmts) in memory formation, it is unclear whether individual Dnmts have unique or redundant functions in long-term memory formation. Furthermore, the downstream processes controlled by Dnmts during memory consolidation have not been investigated. In this study, we demonstrated that Dnmt3a1, the predominant Dnmt in the adult brain, is required for long-term spatial object recognition and contextual fear memory. Using RNA sequencing, we identified an activity-regulated Dnmt3a1-dependent genomic program in which several genes were associated with functional and structural plasticity. Furthermore, we found that some of the identified genes are selectively dependent on Dnmt3a1, but not its isoform Dnmt3a2. Specifically, we identified Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 and further demonstrated the involvement of Nrp1 in hippocampus-dependent memory formation. Importantly, we found that Dnmt3a1 regulates hippocampus-dependent memory via Nrp1. In contrast, Nrp1 overexpression did not rescue memory impairments triggered by reduced Dnmt3a2 levels. Taken together, our study uncovered a Dnmt3a-isoform-specific mechanism in memory formation, identified a novel regulator of memory, and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.

Distinct dynamics of parental 5-hydroxymethylcytosine during human preimplantation development regulate early lineage gene expression

The conversion of DNA 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) by TET enzymes represents a significant epigenetic modification, yet its role in early human embryos remains largely unknown. Here we showed that the early human embryo inherited a significant amount of 5hmCs from an oocyte, which unexpectedly underwent de novo hydroxymethylation during its growth. Furthermore, the generation of 5hmC in the paternal genome after fertilization roughly followed the maternal pattern, which was linked to DNA methylation dynamics and regions of sustained methylation. The 5hmCs persisted until the eight-cell stage and exhibited high enrichment at OTX2 binding sites, whereas knockdown of OTX2 in human embryos compromised the expression of early lineage genes. Specifically, the depletion of 5hmC affected the activation of embryonic genes, which was further evaluated by ectopically expressing mouse Tet3 in human early embryos. These findings revealed distinct dynamics of 5hmC and unravelled its multifaceted functions in early human embryonic development.

Current approaches in CRISPR-Cas systems for diabetes

In the face of advancements in health care and a shift towards healthy lifestyle, diabetes mellitus (DM) still presents as a global health challenge. This chapter explores recent advancements in the areas of genetic and molecular underpinnings of DM, addressing the revolutionary potential of CRISPR-based genome editing technologies. We delve into the multifaceted relationship between genes and molecular pathways contributing to both type1 and type 2 diabetes. We highlight the importance of how improved genetic screening and the identification of susceptibility genes are aiding in early diagnosis and risk stratification. The spotlight then shifts to CRISPR-Cas9, a robust genome editing tool capable of various applications including correcting mutations in type 1 diabetes, enhancing insulin production in T2D, modulating genes associated with metabolism of glucose and insulin sensitivity. Delivery methods for CRISPR to targeted tissues and cells are explored, including viral and non-viral vectors, alongside the exciting possibilities offered by nanocarriers. We conclude by discussing the challenges and ethical considerations surrounding CRISPR-based therapies for DM. These include potential off-target effects, ensuring long-term efficacy and safety, and navigating the ethical implications of human genome modification. This chapter offers a comprehensive perspective on how genetic and molecular insights, coupled with the transformative power of CRISPR, are paving the way for potential cures and novel therapeutic approaches for DM.